The Journalist And the Spies

The murder of a reporter who exposed Pakistan’s secrets.

Pakistani intelligence officials warned Shahzad to curb his reporting, which revealed links between the military and Al Qaeda.Credit Illustration by SEAN MCCABE

On May 30th, as the sun beat down on the plains of eastern Pakistan, a laborer named Muhammad Shafiq walked along the top of a dam on the Upper Jhelum Canal to begin his morning routine of clearing grass and trash that had drifted into the intake grates overnight. The water flow seemed normal, but when he started removing the debris with a crane the machinery seized up. He looked down and saw, trapped in the grates, a human form.

Shafiq called some colleagues, and together they pulled out the body. Occasionally, farmers and water buffalo drown in the canal, float downstream, and get stuck in the grates, but never a man in a suit. “Even his tie and shoes were still on,” Shafiq told me. He called the police, and by the next day they had determined the man’s identity: Syed Saleem Shahzad, a journalist known for his exposés of the Pakistani military. Shahzad had not shown up the previous afternoon for a television interview that was to be taped in Islamabad, a hundred miles to the northwest. His disappearance was being reported on the morning news, his image flashed on television screens across the country. Meanwhile, the zamindar—feudal lord—of a village twenty miles upstream from the dam called the police about a white Toyota Corolla that had been abandoned by the canal, in the shade of a banyan tree. The police discovered that the car belonged to Shahzad. Its doors were locked, and there was no trace of blood.

The previous afternoon, Shahzad had left his apartment, in the placid F-8/4 neighborhood of Islamabad, and driven toward Dunya studios, about five miles away. It was five-thirty; the television interview was scheduled for six. According to a local journalist who talked to a source in one of Pakistan’s cell-phone companies, Shahzad’s phone went dead twelve minutes later. His route passed through some of the country’s most secure neighborhoods, and no one had reported seeing anything suspicious. Some Pakistanis speculated that Shahzad might even have known the people who took him away.

It was a particularly anxious time in Pakistan. Four weeks earlier, American commandos had flown, undetected, into Abbottabad, a military town northwest of Islamabad, and killed Osama bin Laden. The Pakistani Army, which for more than sixty years has portrayed itself as the country’s guardian and guide, was deeply embarrassed: either it had helped to hide bin Laden or it had failed to realize that he was there. Certainly it hadn’t known that the Americans were coming.

Less than three weeks after the Abbottabad raid, the Army was humiliated a second time. A group of militants, armed with rocket-propelled grenades and suicide vests, breached one of the country’s most secure bases, the Pakistan Naval Air Station-Mehran, outside Karachi, and blew up two P-3C Orion surveillance planes that had been bought from the United States. At least ten Pakistanis affiliated with the base died. The components of several nuclear warheads were believed to be housed nearby, and the implication was clear: Pakistan’s nuclear arsenal was not safe. In barracks across the country, military officers questioned the competence of Pakistan’s two most powerful men, General Ashfaq Parvez Kiyani, the chief of the Army staff, and General Ahmad Shuja Pasha, the chief of the Inter-Services Intelligence agency, or I.S.I. Some officers even demanded that the Generals resign. Ordinary Pakistanis, meanwhile, publicly disparaged the one institution that, until then, had seemed to function.

Amid this tumult, Shahzad wrote a sensational story for Asia Times Online, the Web site that employed him, saying that the attack on the Mehran base had been carried out by Al Qaeda—not by the Pakistani Taliban, which had claimed responsibility. He said that the Mehran assault had been intended to punish the military for having conducted “massive internal crackdowns on Al Qaeda affiliates within the Navy.” A number of sailors had been detained for plotting to kill Americans, and one “was believed to have received direct instructions from Hakeemullah Mehsud”—the chief of the Pakistani Taliban. It was not the first time that Shahzad had exposed links between Islamist militants and the armed forces—a connection that Pakistan’s generals have denied for years. But the Mehran article was his biggest provocation yet.

Shahzad, whose parents migrated from India after Partition, making him a muhajir—Urdu for “immigrant”—was an affable outsider within Pakistan’s journalistic circles. Asia Times Online is not connected to any of the country’s established newspapers; its editorial operations are based in Thailand. Shahzad had no local editor to guide him or restrain him. Only a few other journalists had written as aggressively about Islamist extremism in the military, and not all of them had survived.

A hallmark of Shahzad’s reporting was that it frequently featured interviews with Islamist militants, including Al Qaeda fighters. His work was sometimes inaccurate, but it held up often enough so that other journalists followed his leads. Perhaps because he had cultivated so many militants as sources, he occasionally seemed to glorify the men who were carrying out suicide bombings and assassinations. In 2009, he published a breathless account of a meeting with Ilyas Kashmiri, a top Al Qaeda leader. Shahzad noted that the terrorist “cut a striking figure,” was “strongly built,” and had a powerful handshake, adding, “Ilyas, with his unmatched guerrilla expertise, turns the strategic vision into reality, provides the resources and gets targets achieved, but he chooses to remain in the background and very low key.” At other times, like many Pakistani journalists, he seemed to spare the intelligence services from the most damning details in his notebooks. But on several important occasions—as in the case of the Mehran attack—he wrote what appeared to be undiluted truth about the Pakistani state’s deepest dilemmas.

An autopsy report showed that Shahzad had died slowly and painfully, his rib cage smashed on both sides, his lungs and liver ruptured. Someone, apparently, had intended to send a message by killing him.

The media in Pakistan immediately suggested a culprit. According to the newspaper Dawn, it was believed that Shahzad “had been picked up by the I.S.I. because of his recent story on the P.N.S.-Mehran base attack.”

“Well, it strikes me as hilariously ironic that someone as small as me is such a challenge to two people as huge as you!”Buy the print »

Two days after Shahzad’s body was found, an I.S.I. official made a statement denying that its agents had played any role in the killing. Shahzad’s death, he said, was “unfortunate and tragic,” adding, “Baseless accusations against the country’s sensitive agencies for their alleged involvement in Shahzad’s murder are totally unfounded.” Forty-six journalists have been killed in Pakistan since 2001, and the I.S.I. had never before issued such a stark denial. The statement hardly quieted suspicion; in fact, it heightened it. “Everybody knows who did it,” Muhammad Faizan, a colleague of Shahzad’s at Asia Times Online and a friend, told me. “But no one can say.”

I met Saleem Shahzad nine days before he disappeared, and he seemed to know that his time was running out. It was May 20th, and Islamabad was full of conspiracy theories about the Abbottabad raid: bin Laden was still alive; Kiyani and Pasha had secretly helped the Americans with the raid. Mostly, the public radiated anger and shame.

I had called Shahzad to discuss a pair of stories he’d written about bin Laden. In March, five weeks before the raid in Abbottabad, Shahzad claimed that bin Laden had suddenly come across the radar screens of several intelligence agencies: he was on the move. The story also reported that bin Laden had held a strategy meeting with an old friend, Gulbuddin Hekmatyar, an Afghan mujahideen whom the State Department considers a “global terrorist.” Then, just after the Abbottabad raid, Shahzad published a report claiming that the Pakistani leadership had known that the Americans were planning a raid of some sort, and had even helped. What the Pakistanis didn’t know, Shahzad wrote, was that the person the Americans were looking for was bin Laden. Both stories struck me as possibly dubious, but it was clear that Shahzad had numerous sources inside Pakistani intelligence and other intelligence agencies in the region.

Shahzad and I agreed to meet at a Gloria Jean’s coffee shop, not far from his home. For years, Islamabad was a sleepy town of bureaucrats; however dangerous the rest of Pakistan was, the capital was usually quiet. This was no longer true. In 2008, the Marriott Hotel, only a few miles from Gloria Jean’s, was destroyed by a suicide bomber, who killed or wounded more than three hundred people. Lately, the Kohsar Market—the collection of expensive boutiques where the Gloria Jean’s is situated—had been declared off limits for American Embassy personnel on weekends, out of fear that it would be attacked.

Shahzad and I took our coffees upstairs. He pointed to a table in an alcove by a window. “Welcome to my private office,” he said, with a smile. “No one will be able to hear us here.”

We talked for a few minutes about the Abbottabad raid and the stories he’d written. Shahzad was tall and self-possessed; he had thick black hair and a round face offset by a trim beard. He was warm and expressive, the sort of reporter whom people talked to because he seemed genuinely nice. No wonder he got all those scoops, I thought. He was wearing Western clothes and spoke flawless English. He told me that he knew some of my colleagues, and offered to help me out in any way that he could.

And then Shahzad changed the subject. What he really wanted to talk about was his own safety. “Look, I’m in danger,” he said. “I’ve got to get out of Pakistan.” He added that he had a wife and three kids, and they weren’t safe, either. He’d been to London recently, and someone there had promised to help him move to England.

The trouble, he said, had begun on March 25th, the day that he published the story about bin Laden’s being on the move. The next morning, he got a phone call from an officer at the I.S.I., summoning him to the agency’s headquarters, in Aabpara, a neighborhood in eastern Islamabad. When Shahzad showed up, he was met by three I.S.I. officers. The lead man, he said, was a naval officer, Rear Admiral Adnan Nazir, who serves as the head of the I.S.I.’s media division.

“They were very polite,” Shahzad told me. He glanced over his shoulder. “They don’t shout, they don’t threaten you. This is the way they operate. But they were very angry with me.” The I.S.I. officers asked him to write a second story, retracting the first. He refused.

And then Admiral Nazir made a remark so bizarre that Shahzad said he had thought about it every day since.

“We want the world to believe that Osama is dead,” Nazir said.

Bin Laden was still alive, his whereabouts presumably unknown, when that conversation occurred. I pressed Shahzad. What did they mean by that?

He shrugged and glanced over his shoulder again. They were obviously trying to protect bin Laden, he said.

“Do you think the I.S.I. was hiding bin Laden?” I asked him.

Shahzad shrugged again and said yes. But he hadn’t been able to prove it. (The I.S.I. calls this claim an “unsubstantiated accusation of a very serious nature.”)

Shahzad said that he’d left I.S.I. headquarters that day thinking that he needed to be careful. Now, two months later, there was another reason to worry: a book that he’d written, “Inside Al Qaeda and the Taliban,” was being released in three days, in both Pakistan and the West. The book, written in English, explored even more deeply the taboo subject of the I.S.I.’s relationship with Islamist militants.

“They’re going to be really mad,” Shahzad said.

Since the founding of Pakistan, in 1947, one of the country’s central myths has been the indispensability of the Army. Along with its appendage the I.S.I., it has intervened regularly in domestic politics, rigging votes and overthrowing elected governments. Civilians have been viewed by the Army as a collective nuisance, easily undermined or ignored.

In the spring of 1999, when General Pervez Musharraf, then the chief of the Army staff, sent Pakistani soldiers into the Kargil region of India—setting off a war between the two countries—he didn’t even bother telling the Prime Minister, Nawaz Sharif. (Musharraf denies this.) Sharif tried to fire him, but Musharraf threw Sharif in jail and took control of the government. Musharraf ruled for nine years, bullying the Supreme Court and fixing elections, and exhausting the public’s patience for military rule. Since Musharraf left office, in 2008, the military has continued to pay the country’s civilian leaders little respect. In October, 2009, after an attack by Islamist militants on the Army’s headquarters in Rawalpindi, Rehman Malik, Pakistan’s Interior Minister, was prohibited from entering the compound. The country’s current President, Asif Zardari, is seen as serving merely at the military’s pleasure.

Pakistan is one of the world’s poorest countries, but it has the eighth-largest army, which takes up nearly a quarter of the country’s federal budget. The Army’s oligarchs have appropriated a remarkable amount of the country’s wealth; they have substantial investments in the oil-and-gas industry and own shopping centers, farms, banks, and factories. Members of the Army are believed to traffic in narcotics, guns, and mercenaries. Officers live behind high walls, in manicured compounds of a luxury unimaginable to the average Pakistani. Army officers send their children to special schools and avail themselves of special hospitals. “The Pakistani Army is like a mafia,” Ayesha Siddiqa, an independent author who has written extensively about the Pakistani military, said. “The Army has its own interests, and it will eliminate any opposition to those interests, including civilian governments.”

But the most pernicious of the Army’s activities has been its long alliance with Islamist militants. Since the late seventies, the military and the I.S.I. have trained and directed thousands of militants to fight in Indian Kashmir—an area that Pakistan has claimed since independence—and in Afghanistan. For years, the I.S.I. has offered sanctuary to Taliban leaders, who have used Pakistan as a base for planning operations.

In an article published in October, 2010, Shahzad reported that I.S.I. officials knew where top Taliban leaders were hiding in Karachi, yet had done nothing to pick them up. Some Western officials believe that the I.S.I.’s protection extends to the Taliban’s supreme leader, Mullah Omar. In May, a retired senior Pakistani military officer told me that Mullah Omar was living in Pakistan, with the knowledge of the country’s security agencies. “Our people have his address,” he said. The I.S.I. also provides support to the Haqqani network, a Taliban-related guerrilla group. Publicly, Pakistan’s generals claim that they cannot find Taliban and Haqqani leaders. Although many American officials consider this a lie, Pakistan continues to receive as much as three billion dollars a year from the U.S.—most of it for the military.

In recent years, as Pakistan has edged toward anarchy, the I.S.I. has grown bolder and more violent. This spring, a witness testified in federal court in Chicago that I.S.I. agents were deeply involved in the planning of the terrorist attack in Mumbai in 2008, which killed a hundred and sixty-three people. The witness, a Pakistani-American named David Headley, said that he had received espionage training from I.S.I. operatives, and that he had provided hours of video surveillance of the Mumbai target to the I.S.I. and a terrorist group called Lashkar-e-Taiba. Headley testified that he understood Lashkar to be operating “under the umbrella of the I.S.I.” Shortly after the Mumbai attack, Shahzad published an article alleging that the operation was based on an I.S.I. scheme for an attack on another Indian target. At the time, the I.S.I. was under the direction of General Kiyani.

Since the late nineties, the I.S.I.’s links to bin Laden and Al Qaeda have been strong enough to expose some embarrassing entanglements. In 1998, the Clinton Administration fired cruise missiles at a jihadi training camp in Afghanistan, in the hope of killing bin Laden. The missiles missed him, but they killed several Islamist militants—and the team of I.S.I. agents who were training them.

The agency’s links to bin Laden continued after the 9/11 attacks. This May, I travelled to Afghanistan to meet an I.S.I. agent named Fida Muhammad, who had been arrested by Afghan intelligence agents. He was being held in Pul-i-Charki prison, outside Kabul. When I arrived, the Afghan guards brought Muhammad to a small room and left him alone with me and my translator. Muhammad told me that he’d been a prisoner since 2007. He was from Sada, a village in the Federal Administered Tribal Areas of Pakistan, near the border with Afghanistan. He described himself as a civilian employee of the I.S.I. For much of the past decade, he said, he had escorted Haqqani fighters from their sanctuaries in Pakistan into Afghanistan, where they fought against the Americans. He had been hired for his knowledge of the trails that wind through the mountainous border. “I can pass right under the noses of the Americans and the Afghans, and they will never see me,” he said. He’d been arrested while spying on Indian agents inside Afghanistan.

Muhammad told me that his most memorable job came in December, 2001, when he was part of a large I.S.I. operation intended to help jihadi fighters escape from Tora Bora—the mountainous region where bin Laden was trapped for several weeks, until he mysteriously slipped away. Muhammad said that when the American bombing of Tora Bora began, in late November, he and other I.S.I. operatives had gone there, and into other parts of eastern Afghanistan, to evacuate training camps whose occupants included Al Qaeda fighters.

“We told them, ‘Shave your beards, change your clothes, and follow us,’ ” Muhammad said. “We led them to the border with Pakistan and told them they were on their own. And then we went back for more.”

Muhammad was part of a four-man team, and there were dozens of such teams. He estimated that the I.S.I. teams evacuated as many as fifteen hundred militants from Tora Bora and other camps: “Not only Arabs but Pakistanis, Uzbeks, and Chechens. I didn’t see bin Laden. But there were so many Arabs.” The operation had been sanctioned at the highest levels of the I.S.I. “There are people in the I.S.I. who believe the militants are valuable assets,” he said. (The I.S.I. denied Muhammad’s account.)

Amrullah Saleh directed the Afghan intelligence service from 2004 to 2010. He recently told me that in 2005 his men arrested an I.S.I. operative, Syed Akbar Sabir, who had escorted bin Laden from the Pakistani region of Chitral to Peshawar, passing through Kunar Province, in Afghanistan, along the way. “We believed that he was part of the I.S.I. operation to care for bin Laden,” Saleh said. In 2006, Sabir was convicted in an Afghan court of aiding the insurgency, and sentenced to fifteen years in prison. I spoke to him at Pul-i-Charki in May. He told me that he was a trained physician and a member of a militia financed by the Pakistani Army, but he denied that he was an I.S.I. operative.

Since the raid in Abbottabad, U.S. officials have openly suggested that the Pakistani Army or the I.S.I. helped to hide bin Laden, but hard evidence has yet to be found. Perhaps the most suggestive hint of official involvement comes in the shadowy figure of Lieutenant General Nadeem Taj, who was the director of the I.S.I. in 2007 and 2008. He was very close to Musharraf—they are reportedly related by marriage. Bruce Riedel, a former C.I.A. officer, says that Taj was deeply involved with Pakistani militants, particularly those fighting against India. Riedel, who oversaw President Barack Obama’s initial review of strategy in Afghanistan and Pakistan, said, “Taj was very close to the militant networks. And his fingerprints were on everything.” In 2008, American officials successfully pressured Musharraf to remove Taj, suspecting that he had been involved in the bombing of the Indian Embassy in Kabul, earlier that year.

Before taking over the I.S.I., Taj was the commandant of the Pakistani military academy in Abbottabad. That is, he was the senior military official in Abbottabad at the time that American officials believe bin Laden began living there. Taj retired from the Pakistani Army in April, just days before the raid in Abbottabad. Attempts to track him down in Pakistan were unsuccessful.

Riedel said, “Taj is the right person at the right time. If the I.S.I. was helping to hide bin Laden, then it would make sense to park him somewhere permanently. Who better to be the park policeman than Musharraf’s favorite general?”

Shahzad was not the only Pakistani journalist whose reporting made him a target of the state. Umar Cheema, a reporter for the News, an important Pakistani daily, has published numerous articles on the military’s failures. At three in the morning on September 4, 2010, Cheema was driving home from a tea shop in Islamabad, where he’d met some friends, when he was forced off the road by two unmarked Toyotas. Two men in police uniforms approached his car. They told him that he was suspected of running over and killing a pedestrian.

The policemen directed Cheema into the back seat of a black Land Cruiser, where two other men handcuffed him and covered his face with a shawl. After two hours, the car came to a stop. He was led up a stairwell, and a heavy door closed behind him. Cheema asked, “What police station have we come to?” One of the men responded, “Shut up.” “That’s when I knew I was in trouble,” Cheema told me. During the next half hour, he was stripped, beaten with rods and a leather strap, and sexually humiliated. “I was crying out to God,” Cheema recalled. Then the shawl covering his face was removed: standing around him were five masked men. They shaved his head and eyebrows and took degrading photographs of him. “We’re going to make an example of you,” one of the men said.

Cheema, who is thirty-four, described his ordeal over tea at my hotel in Islamabad. He spoke without hesitation, and seemed remarkably fit, given all that he’d been through.

The torturers, Cheema said, put the shawl back over his face and drove him to a village a hundred miles from Islamabad. One of the men removed the cuffs and told him to walk into the street. “You’ll find your car right over there,” the man said. “Don’t look back.” They’d taken Cheema’s glasses, wallet, and cell phone, and given him a hundred rupees—the equivalent of a dollar and twenty cents. “That was for the toll on the way home,” he said.

Cheema’s captors made it clear that they were working for the government. “You are being punished for your reporting,” one of them said during the interrogation. Cheema had no doubt that he had been detained by the I.S.I.; ten times over the previous six months, he told me, the agency had warned associates of his that it was unhappy about his reporting. (The I.S.I. denied that it had anything to do with the assault.)

Pakistani journalists say that it is not easy to predict when the security agencies will detain, torture, or kill a reporter. Pakistan is a peculiar state: it is unjust and autocratic, but it is also partly open and partly democratic. The media there is loud, lively, and varied, and there are good newspapers, magazines, and television networks that investigate official misconduct. And although reporters in Pakistan are routinely threatened and sometimes brutalized, a small cohort seems able to write more freely about sensitive subjects.

The journalist best known outside Pakistan is Ahmed Rashid, the author of several books on Pakistan and Afghanistan; his book “Taliban” was a best-seller in the U.S. He has published dozens of revelatory reports on the military and intelligence services. Rashid says that he has been threatened repeatedly by the I.S.I. over the years, and was once warned personally by Musharraf. Rashid’s colleagues believe that his prominence in the West has protected him; he writes regularly for The New York Review of Books and the Financial Times.

These days, Rashid says, he has had to be more careful. After a recent threat, he stayed out of Pakistan for a couple of months before returning to his home, in Lahore. “There is a red line in Pakistan—there has always been a red line,” Rashid said. “But, after Saleem Shahzad, no one knows where the red line is anymore.” He went on, “It’s debilitating. You can’t really go out and report. Sometimes you just sit and think about what is going to happen.”

Saleem Shahzad wasn’t well known outside the country. Asia Times Online, which he joined in 2000, had only a small presence in Pakistan, and was struggling to attract international readers. Shahzad seemed to enjoy the freedom that the Web site offered, even if it meant that he had to surrender some influence. In the preface to “Inside Al Qaeda and the Taliban,” he wrote, “Independent reporting for the alternative media best suits my temperament as it encourages me to seek the truth beyond ‘conventional wisdom.’ As a result, I study people and situations from a relatively uncompromised position.”

In the decade after 9/11, Shahzad’s reporting increasingly attracted notice within Pakistani media circles. Many of his articles for Asia Times Online were reprinted in the Pakistani press. What stood out was his legwork: he often travelled to the tribal areas near the Afghan border to meet with members of the Taliban and Al Qaeda. Zafar Sheikh, Shahzad’s best friend and a local correspondent for the Saudi state television network, told me, “Saleem would say, ‘Let’s have a joyride!,’ and then we would go off to somewhere crazy to meet the militants.” Shahzad took to the rugged life. During the government’s offensive against militants in the Swat Valley, in 2009, rebels were impressed by his ability to sleep, untroubled, for hours in the open air.

Sheikh warned Shahzad that the stories he was writing could get him in trouble with the authorities. “I told him so many times, ‘Saleem, you’re going to be killed, what you’re doing is too dangerous,’ but he was reckless.”

“I couldn’t find a nail file, like you asked, so I brought you some nail polish and lip gloss instead.”Buy the print »

In September, 2009, Pakistani officials announced that Ilyas Kashmiri, the Al Qaeda operative, had been killed in a drone strike. On October 15th, Shahzad published a memorable rebuttal—his account of meeting Kashmiri, with a dateline from North Waziristan. “We planned this battle to bring the Great Satan and its allies into this swamp,” Kashmiri told him. Shahzad got the story right: Kashmiri was still alive. The article’s tone bordered on gloating. Shahzad wrote that Kashmiri’s arrival in the border areas would send “a chill down spines in Washington as they realized that with his vast experience, he could turn unsophisticated battle patterns in Afghanistan into audacious modern guerrilla warfare.”

Tony Allison, a South African who works in the Thailand offices of Asia Times Online, was Shahzad’s editor. “Sometimes, Saleem would disappear for three or four days, and I wouldn’t know where he’d gone, and then he would emerge with a great story,” he told me. “I knew he could get the story and I trusted him.”

Shahzad was not universally respected by his peers. No doubt there was some resentment over his scoops. But sometimes he seemed to be regurgitating the stories his sources told him without checking whether they were true. Sometimes he got things seriously wrong. His story claiming that Pakistan’s leaders assisted the Americans’ raid in Abbottabad, for instance, is not supported by any available evidence.

“I liked Saleem, but I didn’t always know what was right and what was wrong,” Cyril Almeida, the chief political columnist for Dawn, told me. “It was difficult to know where he was getting this stuff.”

In Shahzad’s book, there are many vivid anecdotes; for instance, he details an incident in which an Al Qaeda militant and former Army officer, Major Haroon Ashik, smuggled a shipment of night-vision goggles through Islamabad International Airport, assisted by an aide to President Musharraf. The story seems solid, as it is based on an interview with Ashik. But the book’s analysis is shallow: Shahzad depicts Al Qaeda not as an embattled and fragmented entity, as most of the available evidence suggests it is, but, rather, as an Islamist version of SPECTRE, from the James Bond films—a monolithic, secretive power whose influence stretches across the globe. Similarly, instead of portraying the group as a far-flung franchise operation, as it is widely seen in the West, he claims that Al Qaeda has been intimately involved in directing other militant groups in the region, including the Taliban.

Shahzad’s book, even more than his daily journalism, leaves the impression that he harbored sympathy for the killers he writes about. Not only does he describe with enthusiasm the exploits of Taliban and Al Qaeda fighters like Ilyas Kashmiri; he refers several times to “Khurasan”—an outdated term for Central Asia that Al Qaeda followers often use to denote the region. At the end of the book, Shahzad writes, in an oddly prophetic register, “The promised messiah, the Mahdi, will then rise in the Middle East and Al Qaeda will mobilize its forces from Ancient Khurasan for the liberation of Palestine, where a final victory will guarantee the revival of a Global Muslim Caliphate.”

When Shahzad was in college, he was a member of the student wing of Jamaat-e-Islami, an Islamist political party that has fed thousands of recruits into militant groups. Some of his classmates received training as guerrilla fighters, and Shahzad told other journalists that these young men became key sources for his reporting in the field. In recent years, friends and colleagues say, Shahzad stopped supporting Jamaat-e-Islami, finding its ideology too radical.

Although Shahzad didn’t support the militants’ aims, his feelings for them ran deep. “I think Saleem had great sympathy for the militants, not because he believed in the caliphate but because he understood their side of the story,” Allison, his editor at Asia Times Online, said. “He understood and empathized with them. He had empathy for the Western soldiers in Afghanistan, too. This is why he was trusted by the militants. He did not share their vision, but he understood their vision.”

Shahzad was socially conservative: he didn’t drink, and friends and colleagues describe him as pious. But they say that he didn’t support Islamist violence. “Saleem felt that there was a kind of endgame unfolding between the militants and the Americans, because the Americans had been so stupid in Afghanistan,” Hameed Haroon, the publisher of Dawn, told me. “This permeated his writing. But he was against the terror.”

Because Shahzad had relationships with a number of I.S.I. agents, he was one of a small class of reporters more likely to become targets of the intelligence agencies. Talking to the I.S.I. allowed him to get privileged information, and to verify information that he had picked up on his own. But maintaining a relationship with the I.S.I. may have created expectations of loyalty. Almeida, the Dawn columnist, told me that he refuses to talk to the I.S.I.: “Once you start talking to these people, that creates a relationship, and then they think you owe them. Then, if you do something they don’t like, they feel betrayed.”

Ayesha Siddiqa, the independent author who has written scathingly of the military, said that, two years ago, she turned down an offer to meet General Pasha, the I.S.I. chief. “Once you go into the headquarters, they have you,” she told me. “They can photograph you there, they can put out the word that you were visiting, they can blackmail you.” Siddiqa, too, has been threatened repeatedly by associates of the military and the I.S.I. Since Shahzad’s death, she has felt more pressure than ever before. “It wears on me,” she said. “Some days, you can’t work. I know that they could come for me anytime.”

Siddiqa spoke to Shahzad only hours before he disappeared. At about 4 P.M. on May 29th, he called her on her cell phone. She was driving, she said, so the conversation was brief. Shahzad seemed interested in some aspect of official Pakistani duplicity. She recalls him saying, “Pakistan should stop lying to the U.S.—even if we don’t want to do what they want us to do, we should stop lying about it.” They agreed to speak later that day.

According to Shahzad’s friends and colleagues, he had been warned by the I.S.I. at least three times before he finally disappeared. Shahzad documented one of those encounters in remarkable detail.

On October 16, 2010, Shahzad published an article about Abdul Ghani Baradar, then the deputy commander of the Taliban. The next day, he was summoned to the I.S.I.’s headquarters. The Baradar story touched on the I.S.I.’s relationship with Taliban leaders—an extremely sensitive subject. Earlier that year, American and Pakistani intelligence agents had arrested Baradar during a raid in Karachi. At the time, both the Americans and the Pakistanis hailed Baradar’s arrest as a breakthrough in their difficult relationship. But I.S.I. agents later told a different story: they had orchestrated Baradar’s arrest, after discovering that he was holding secret peace talks with Afghanistan’s leaders, without informing his I.S.I. handlers. The I.S.I. agents had set up the raid in Karachi in order to cut off the peace talks. Shahzad, in his October article, wrote that the I.S.I. had quietly released Baradar.

After a tense meeting with two I.S.I. officers about the article, Shahzad called Ali Dayan Hasan, the director of Human Rights Watch in Pakistan. Hasan suggested that Shahzad make notes of the meeting. Shahzad did so, and sent a copy of them to Hasan. Shahzad wrote that he was met at headquarters by two I.S.I. officials—Commodore Khalid Pervaiz and Rear Admiral Nazir, the same officer who gave him the warning in March.

Nazir and Pervaiz were courteous as they asked him to reveal his sources for the Baradar story. Shahzad refused. They asked him to publicly retract the story, and Shahzad refused to do that, too. The I.S.I. officers did not push him, he wrote.

But at the very end of the conversation Nazir made an ominous remark. He said, “We recently arrested a terrorist and recovered a lot of data—diaries and other material—during the interrogation. The terrorist had a hit list with him.” He then added, “If I find your name on the list, I will certainly let you know.”

Seven months later, on May 22nd, the naval base at Mehran came under attack. The siege lasted fifteen hours and was covered, live, on Pakistani television. Footage shot by cameramen just outside the base showed plumes of fire from the ruined jets spiralling into the night sky.

Five days after the incident, Shahzad published his report saying that the attack was a reprisal for the Navy’s arrest of sailors who were Al Qaeda sympathizers. High-level naval officers, Shahzad wrote, had been secretly negotiating with Al Qaeda over the fate of the detained sailors. To move the discussions along, militants had already carried out three attacks on naval targets in Karachi.

Shahzad quoted naval officers as saying that the arrest of the Islamist sailors had set off a chain reaction. “That was the beginning of huge trouble,” one officer told Shahzad. According to the article, top officers in the Navy believed that the ease with which the militants had attacked the naval base indicated there was a “sizable Al Qaeda infiltration within the Navy’s ranks.” Indeed, Shahzad wrote, the Mehran attack had been carried out by a group of fighters led by Ilyas Kashmiri—the Al Qaeda fighter whom he had praised for his “unmatched guerrilla expertise.”

Three days after the attack, the naval base at Mehran got a new commander: Commodore Pervaiz, one of the two I.S.I. officers who, in October, had warned Shahzad to tone down his reporting. The embarrassing Asia Times Online report was published on Pervaiz’s second day in command. Two days later, Shahzad disappeared.

Commodore Zafar Iqbal, an I.S.I. spokesman, told me that Pervaiz would not be available for an interview. “Out of the question,” he said.

The Islamization of the Pakistani military causes deep worry among policymakers in the United States and Europe. Pakistan, which is believed to possess about a hundred nuclear warheads, has the fastest-growing atomic arsenal in the world. The fear is that rogue members of the military could help a terrorist group like Al Qaeda acquire a warhead, or that a group of Islamist military officers could overthrow the government. “The Pakistanis are worried to death about the security of their nuclear weapons,” a senior American military officer told me. “They would never tell us that, but we are sure of it.”

Even before the attack on Mehran, there had been signs of violent radicalism inside the Pakistani military. Two assassination attempts against President Musharraf in 2003, both of which nearly succeeded, were carried out by Al Qaeda fighters who were assisted by Air Force officers. And in October, 2009, came the attack on the Army’s headquarters in Rawalpindi, killing twenty-three people. The attackers wore Army uniforms and seemed to know the layout of the headquarters. One of the lead attackers was a former medic in the Pakistani Army.

Shahzad argues in his book that it was around the time of the attempts on Musharraf’s life that Al Qaeda made its first substantial inroads into the Army. “From 2003 onwards Al Qaeda succeeded in sowing the seeds of dissent within Pakistan’s armed forces,” Shahzad writes. “Pakistan’s tribal youths and formerly pro-establishment jihadi cadres moved away from Pakistan’s ruling establishment and promised allegiance to Al Qaeda.”

In the weeks after the Abbottabad raid, Islamist groups tried to capitalize on the outpouring of anti-American anger inside the Pakistani military. The most active group appears to have been Hizb ut-Tahrir, a global movement that advocates a peaceful restoration of the caliphate, the theocratic state that once ruled the Islamic world from Spain to the Arabian Sea. Hizb ut-Tahrir is banned in Pakistan, but it is allowed to operate in many countries, including the United Kingdom.

After the attack on the Mehran base, people working on behalf of Hizb ut-Tahrir distributed leaflets at military bases and in cantonments in Karachi, with the aim of stirring up a revolt. One leaflet said, “O true officers of the Pakistan Army! Your leaders broke their promises again. . . . These traitorous leaders are spilling your blood and the blood of Muslims in Afghanistan and the tribal areas, and they are doing this for America. . . . This is a request for you to prepare a plan to give power to Hizb ut-Tahrir.” The incidents, which took place on May 3rd, May 7th, and June 23rd, were confirmed by Commodore Iqbal.

Pakistan’s military leaders have become acutely nervous about Hizb ut-Tahrir, and about the Islamist threat more generally. In June, they announced the arrest of Brigadier Ali Khan, who worked at Army headquarters, because of alleged associations with Hizb ut-Tahrir. According to Pakistani press accounts, Brigadier Khan had denounced Kiyani and Pasha in language similar to that used in the leaflets.

Iqbal told me that Khan’s arrest was approved at the highest levels. “You don’t just arrest a brigadier,” he said. “It’s a very big deal.” Some American officials believe that the arrest of Khan, who was only months from retirement, was designed to send a message to lower-ranking officers that Islamist sentiment—and insubordination—would not be tolerated. “Khan was a fall guy,” the senior American military officer told me. Khan’s arrest may have been ordered to reassure the U.S. as well. American officials say that Kiyani and Pasha, for all their faults, are the best allies the U.S. is likely to get.

The attack on the Mehran base was especially troubling, because it could be seen as a test run for an assault on one of Pakistan’s nuclear bases. “You have to appreciate how impressive the attack in Karachi was,” the senior American military officer said. “They practiced it. They knew the layout of the base. They probably built a mock-up of the place. And no one knew a thing.”

Commodore Iqbal did not rule out the possibility that the attackers were helped by Al Qaeda sympathizers inside the base, but said that there was “no proof” yet. At least three Pakistani sailors have been court-martialled.

The presence of Islamists in the Navy, and at Mehran, was not a secret among Pakistanis. But Shahzad’s article was particularly incendiary. Not only did he report that sailors at the base had helped the attackers; he wrote that the Navy’s leadership was bargaining directly with Al Qaeda. “Consider the time when Saleem’s piece came out,” a high-level American official told me. “The military felt humiliated. It felt backed into a corner.” The official added, “When you’re backed into a corner like that, you strike back.”

The first order to harm Shahzad was issued shortly after his article on the Mehran attack appeared. The initial directive was not to kill him but to rough him up, possibly in the same way that Cheema had been dealt with. But a senior American official confirms that, at some point before Shahzad was taken away, the directive was changed. He was to be murdered.

Five weeks after the killing, Admiral Mike Mullen, the chairman of the Joint Chiefs of Staff, said publicly that it had been “sanctioned by the government” of Pakistan. In fact, according to the American official, reliable intelligence indicates that the order to kill Shahzad came from a senior officer on General Kiyani’s staff. The officer made it clear that he was speaking on behalf of Kiyani himself. (General Athar Abbas, the spokesman for the Pakistani Army, called this allegation “preposterous.”)

After the discovery of Shahzad’s body, some of his friends and family members told me they believed that the I.S.I. agents had meant only to beat him, and that things got out of hand. They had reason to think so. A year earlier, during an altercation with a guard outside a social club in Islamabad, Shahzad had been shot. Shahzad’s brother-in-law, Hamza Ameer, told me that the guard had become angry after Shahzad complained about being denied entry, because he had forgotten his membership card. The bullet had penetrated his liver, and it remained lodged near his spine. (According to Ameer, Shahzad eventually pardoned the guard in a Pakistani court, as is allowed under the law, so the guard went free.) Shahzad’s autopsy report says that a ruptured liver is one of the things that killed him.

But Dr. Mohammed Farrukh Kamal, one of the physicians who performed the autopsy, told me that Shahzad had been beaten with a heavy instrument, like a metal rod, and he dismissed the notion that Shahzad had been killed by mistake. “You don’t hit a person that hard by accident,” he told me. “They meant to kill him.”

Shahzad’s journalism may not have been the sole reason that he was targeted. I.S.I. officials may have become convinced that Shahzad was working for a foreign intelligence agency. This could have elevated him in the eyes of the military from a troublesome reporter who deserved a beating to a foreign agent who needed to be killed.

In fact, Shahzad, at the time of his death, was in contact with several foreign intelligence officials. He told me that a Saudi intelligence official was among those who had told him that bin Laden had met with Gulbuddin Hekmatyar, the mujahideen now considered a terrorist. Shahzad himself, under questioning from the I.S.I., had admitted that another source for that story was General Bismillah Khan—then the Interior Minister of Afghanistan, and a loathed figure in the Pakistani military.

More crucially, it appears that, in the months before Shahzad was killed, some foreign intelligence agencies tried to recruit him. Roger van Zwanenberg, the publisher of Pluto Press, the London imprint that released Shahzad’s book, told me that members of British intelligence had asked Shahzad for help during a short visit that he made to London in March. The intelligence officers wanted Shahzad to help them get in touch with Taliban leaders. “Saleem declined,” van Zwanenberg said. He added that, when Shahzad attended a conference in New Delhi this spring, officers from an Indian intelligence agency offered to put him on a retainer. Several of Shahzad’s colleagues confirmed this.

There is no evidence that Shahzad was working for any foreign intelligence agency, but mere suspicion on this front could have imperilled him. “What is the final thing that earns Shahzad a red card—the final thing that tips him over from being a nuisance to an enemy?” a Western researcher in Islamabad said to me. “If someone concluded that he was a foreign agent, and that the stories he was putting out were part of a deliberate effort to defame the I.S.I. and undermine the I.S.I.’s carefully crafted information strategy—if anyone in the I.S.I. concluded that, then Saleem would be in grave danger.”

On June 3rd, four days after Shahzad was found in the Upper Jhelum Canal, a C.I.A. officer, operating a pilotless drone, fired a missile at a group of men who had gathered in an orchard outside the village of Ghwa Khwa, in South Waziristan. Locals who ran to the scene saw many bodies, but a group of militants who had survived told them to stay back. “Kashmiri Khan! Kashmiri Khan!” one of them yelled. Among the dead was Ilyas Kashmiri—the terrorist whom Shahzad had once proved to be still alive, and who he said was responsible for the attack on the Mehran base.

Three days later, Rehman Malik, Pakistan’s Interior Minister, announced that, this time, Kashmiri was definitely dead.

Given the brief time that passed between Shahzad’s death and Kashmiri’s, a question inevitably arose: Did the Americans find Kashmiri on their own? Or did they benefit from information obtained by the I.S.I. during its detention of Shahzad? If so, Shahzad’s death would be not just a terrible example of Pakistani state brutality; it would be a terrible example of the collateral damage sustained in America’s war on terror.

If the C.I.A. killed Kashmiri using information extracted from Shahzad, it would not be the first time that the agency had made use of a brutal interrogation. In 2002, Ibn al-Shaykh al-Libi, an Al Qaeda operative held by the Egyptian government, made statements, under torture, suggesting links between Saddam Hussein and bin Laden; this information was used to help justify the invasion of Iraq.

Kashmiri, who was forty-seven, was a guerrilla fighter who received training from both the Pakistani Army and the I.S.I. According to American officials, he fought in the guerrilla war inside Indian Kashmir, working closely with the I.S.I. According to one frequently heard story, Kashmiri, returning from an operation in India, presented Musharraf—then the chief of the Army staff—with the head of an Indian soldier.

But, as Musharraf began to curtail the activities of militant groups operating in India, Kashmiri moved to the tribal areas and started waging war against the Pakistani state. He brought together the 313 Brigade, an amalgam of Al Qaeda, Taliban, and other fighters. Kashmiri was accused of playing a key role in one of the two unsuccessful plots to assassinate Musharraf in 2003, and he is believed to have helped orchestrate the 2009 attack on the Army’s headquarters. Earlier this year, David Headley, the Pakistani-American who testified in Chicago about the Mumbai attack, named Kashmiri as a key terrorist planner.

On May 27th, Secretary of State Hillary Clinton visited Islamabad, and she presented to Pakistani leaders a list of high-value targets. According to ABC News, Kashmiri was on the list. That morning, Shahzad had published the article naming Kashmiri as the perpetrator of the attack on the Mehran base—broadcasting, once again, his connection to the militant leader.

Bruce Riedel, the former C.I.A. officer, said, “After the Abbottabad raid, the Pakistanis were under enormous pressure to show that they were serious about Al Qaeda.”

Shahzad, at the time of his death, was in contact with several Taliban and Al Qaeda militants. It’s obvious from his book that Kashmiri was one of them. Muhammad Faizan, Shahzad’s colleague, said, “The militants used to call him, not the other way around.”

After Shahzad’s murder, the Pakistani government appointed a commission, led by a justice of the Supreme Court, to investigate. In late July, the justice, Mian Saqib Nisar, summoned a group of Pakistani reporters and editors and briefed them on his progress. Bani Amin Khan, the inspector general of the Islamabad police, also appeared at the meeting, with some of his investigators. According to reporters who attended the briefing, one of the investigators said that he had seen something unusual in Shahzad’s cell-phone records: more than two hundred and fifty-eight calls to and from a single number during a one-month period.

Imtiaz Alam, the secretary-general of the South Asian Free Media Association, told me that after the briefing he approached Khan and pressed him for details. Khan’s answer, according to Alam: “The calls were with Ilyas Kashmiri.” When I asked Khan about Shahzad’s case, he threw me out of his office.

The evidence is fragmentary, but it is not difficult to imagine a scenario in which Pakistani intelligence agents gave the C.I.A. at least some of the information that pinpointed Kashmiri. Likewise, it seems possible that at least some of that information may have come from Shahzad, either during his lethal interrogation or from data taken from his cell phone. In the past, the I.S.I. and the C.I.A. have coöperated extensively on the U.S. drone program.

This relationship has been strained since the bin Laden killing. For the moment, much of the drone program, once based in Pakistan, appears to be frozen. According to the senior American military officer, the drones are no longer flying out of Shamsi Air Base, in Pakistan, but from Afghanistan, and the intelligence used to target militants is now being collected almost entirely by American networks. Most of the drone strikes are being carried out without prior Pakistani knowledge.

“We want the Pakistanis’ coöperation, but we are prepared to go without it,” the military officer told me. The Americans’ unilateral approach to drone strikes is causing intense tension with Pakistani leaders, and not just because of their claims that the strikes kill many civilians. The drone strikes sometimes reveal that the Americans and the I.S.I. are working against each other.

On March 17th, four missiles fired from a drone hit a group of men who had gathered at a market in the village of Datta Khel, in North Waziristan. As many as forty-four people died. The Pakistani government denounced the strike, claiming that it had killed a number of tribal elders, and demanded an apology.

As with nearly all drone strikes, the precise number and nature of the casualties were impossible to verify. The high-level American official told me that the “tribal elders” were actually insurgent leaders. But he offered another reason that the Pakistani officials were so inflamed: “It turns out there were some I.S.I. guys who were there with the insurgent leaders. We killed them, too.” (The I.S.I. denied that its agents were present.)

What were I.S.I. agents doing at a meeting of insurgent commanders? The American official said that he did not know.

A senior counterterrorism official said that the Kashmiri strike was not connected to Shahzad’s death. At the same time, the official acknowledged that in the past the U.S. had received intelligence from the Pakistanis on Kashmiri, and confirmed that the Pakistanis continue to share information on targets.

Commodore Iqbal, the I.S.I. spokesman, reiterated the agency’s insistence that it had no involvement in Shahzad’s death. But he said that the C.I.A. and the I.S.I. were still coöperating. “We are giving the Americans a lot of intelligence,” Iqbal told me. “We don’t feel like we are getting much in return.” When I asked him if the I.S.I. had coöperated on the strike that killed Kashmiri, he said, “I can’t answer that.”

These days, the high-level American official told me, most drone attacks in Pakistan are “signature strikes,” which are carried out when a group of people match a certain profile—they are operating a training camp, for instance, or consorting with known militants. Such strikes are not directed at specific individuals—like, say, Ayman al-Zawahiri, Al Qaeda’s new leader. Usually, the agency doesn’t know the identities of the people it is firing at. “Most of the high-value targets have been killed this way,” the American official told me.

In the case of Kashmiri, the American official initially told me that he had been killed in a signature strike. “We did the strike, and we found out later that it was him,” the official said. When I pressed him, though, he said, “We sort of thought he would be there.” He declined to elaborate.

Bruce Riedel, the former C.I.A. officer, said that helping the agency kill Kashmiri would have made eminent sense to the I.S.I. Kashmiri had become an enemy of the Pakistani state, and had maintained potentially embarrassing contacts with Pakistani security services.

“If you start from the premise that the Pakistanis had something to do with hiding bin Laden, then you have to assume that they were trying very hard to put everything back into the tube,” Riedel said. “And so it would have made sense for them to get rid of Saleem Shahzad. And Kashmiri, too.”

In Pakistan, reporting on Shahzad’s case ceased, for the most part, after a few weeks. Shahzad’s wife, Anita, recently communicated with me, via e-mail. “I don’t want to rewind to that bitter time,” she said, adding that Shahzad had been “a brave man.” She assured me that “here in Pakistan they are trying their level best to find the culprit.”

In the wake of Shahzad’s death and the Abbottabad raid, the tone of the Pakistani press darkened. Some columnists argued that the Pakistani state was poised to fall to Islamist militants. Ayman al-Zawahiri “is the man waiting to become the caliph of Pakistan,” Khaled Ahmed wrote in the Friday Times, an influential weekly.

This spring, Umar Cheema, still recovering from his ordeal with the I.S.I., was invited to the U.S., where he was honored by Syracuse University for his journalism. Cheema told me that while in America he was offered several fellowships, as well as the prospect of asylum. He decided to come home. “If Pakistan were not in such dark shape, I would leave,” he told me. “But it is my duty to try to make this a better country for the next generation.” He quickly broke a number of important stories, including one charging that Yousaf Raza Gilani, the Prime Minister, and the twenty-five members of his cabinet paid no taxes last year.

Zafar Sheikh, Shahzad’s friend and colleague, took a different path. Years ago, Sheikh said, he regularly accompanied Shahzad on road trips to the tribal areas, and sat in mud huts and interviewed Taliban commanders. He, too, had aspired to write revelatory stories about the inner workings of the I.S.I. But now he has set those ambitions aside.

“I used to be a brave journalist,” Sheikh told me one day as we rode in a car across the Punjabi plains. “But I will be frank with you. I don’t want to get killed like Saleem. I don’t want to suffer like Saleem did. So I’m not part of the war anymore. I am just writing stereotypical bullshit stories—and no one is angry.”

We drove on for a little longer, toward the Upper Jhelum Canal, and, a few minutes later, we found the place where the laborer had discovered Shahzad’s body. The water was streaming into the intake grates.

“I used to look for stories that would open people’s eyes,” Sheikh said. “Now I am just a stupid correspondent doing stupid stories. And I am happy. I am happy.” ♦